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2020 – today
- 2024
[j47]Chunjiang Yu, Hui Zong, Yalan Chen, Yibin Zhou, Xingyun Liu, Yuxin Lin, Jiakun Li, Xiaonan Zheng, Hua Min, Bairong Shen
:
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data. Briefings Bioinform. 25(3) (2024)- [j46]Jianchao Duan, Peiyi Li, Aibin Shao, Xuechao Hao, Ruihao Zhou, Cheng Bi, Xingyun Liu, Weimin Li, Huadong Zhu, Guo Chen, Bairong Shen, Tao Zhu:
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications. Database J. Biol. Databases Curation 2024 (2024) - [j45]Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen:
DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. Database J. Biol. Databases Curation 2024 (2024) - [j44]Shumin Ren, Jiakun Li, Julián Dorado, Alejandro Pazos Sierra, Humberto González Díaz, Aliuska Duardo-Sánchez, Bairong Shen:
From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine. Health Inf. Sci. Syst. 12(1): 6 (2024) - [j43]Hui Zong, Rongrong Wu, Jiaxue Cha, Weizhe Feng, Erman Wu, Jiakun Li, Aibin Shao, Liang Tao, Zuofeng Li, Buzhou Tang, Bairong Shen:
Advancing Chinese biomedical text mining with community challenges. J. Biomed. Informatics 157: 104716 (2024) - [i1]Hui Zong, Rongrong Wu, Jiaxue Cha, Erman Wu, Jiakun Li, Liang Tao, Zuofeng Li, Buzhou Tang, Bairong Shen:
Advancing Biomedical Text Mining with Community Challenges. CoRR abs/2403.04261 (2024) - 2023
- [j42]Ke Shen, Ahmad Ud Din, Baivab Sinha, Yi Zhou, Fuliang Qian, Bairong Shen:
Translational informatics for human microbiota: data resources, models and applications. Briefings Bioinform. 24(3) (2023) - [j41]Chaoying Zhan, Kai Liu, Yuxin Zhang, Yingbo Zhang, Mengqiao He, Rongrong Wu, Cheng Bi, Bairong Shen:
Myocardial infarction unveiled: Key miRNA players screened by a novel lncRNA-miRNA-mRNA network model. Comput. Biol. Medicine 160: 106987 (2023) - [j40]Tong Tang, Xingyun Liu, Rongrong Wu, Li Shen, Shumin Ren, Bairong Shen:
CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs. Genom. Proteom. Bioinform. 21(2): 292-299 (2023) - [j39]Chunjiang Yu, Xin Qi, Wenying Yan, Wentao Wu, Bairong Shen:
Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data. IEEE ACM Trans. Comput. Biol. Bioinform. 20(1): 576-585 (2023) - 2022
- [j38]Shumin Ren, Yanwen Jin, Yalan Chen, Bairong Shen:
CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications. Bioinform. 38(6): 1669-1676 (2022) - [j37]Xiaonan Zheng, Hang Xu, Tianhai Lin, Ping Tan, Qiao Xiong, Xianyanling Yi, Shi Qiu, Lu Yang, Bairong Shen, Jianzhong Ai, Qiang Wei:
CD93 orchestrates the tumor microenvironment and predicts the molecular subtype and therapy response of bladder cancer. Comput. Biol. Medicine 147: 105727 (2022) - [j36]Erman Wu, Xuemeng Fan, Tong Tang, Jingjing Li, Jiao Wang, Xingyun Liu, Zayatta Zungar, Jiaojiao Ren, Cong Wu, Bairong Shen:
Biomarkers discovery for endometrial cancer: A graph convolutional sample network method. Comput. Biol. Medicine 150: 106200 (2022) - 2021
- [j35]Jing Chen, Xingyun Liu, Li Shen, Yuxin Lin, Bairong Shen:
CMBD: a manually curated cancer metabolic biomarker knowledge database. Database J. Biol. Databases Curation 2021 (2021) - [j34]Hongxin He, Manhong Shi, Yuxin Lin, Chaoying Zhan, Rongrong Wu, Cheng Bi, Xingyun Liu, Shumin Ren, Bairong Shen:
HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications. Bioinform. 37(23): 4534-4539 (2021) - [j33]Yalan Chen, Chunjiang Yu, Xingyun Liu, Ting Xi, Guangfei Xu, Yan Sun, Fei Zhu, Bairong Shen:
PCLiON: An Ontology for Data Standardization and Sharing of Prostate Cancer Associated Lifestyles. Int. J. Medical Informatics 145: 104332 (2021) - 2020
- [j32]Xin Qi, Yuxin Lin, Jiajia Chen, Bairong Shen:
Decoding competing endogenous RNA networks for cancer biomarker discovery. Briefings Bioinform. 21(2): 441-457 (2020) - [j31]Rongrong Wu, Yuxin Lin, Xingyun Liu, Chaoying Zhan, Hongxin He, Manhong Shi, Zhi Jiang, Bairong Shen:
Phenotype-genotype network construction and characterization: a case study of cardiovascular diseases and associated non-coding RNAs. Database J. Biol. Databases Curation 2020: baz147 (2020) - [j30]Yalan Chen, Xingyun Liu, Yijun Yu, Chunjiang Yu, Lan Yang, Yuxin Lin, Ting Xi, Ziyun Ye, Zhe Feng, Bairong Shen:
PCaLiStDB: a lifestyle database for precision prevention of prostate cancer. Database J. Biol. Databases Curation 2020: baz154 (2020) - [j29]Lan Yang, Yang Yang, Xingyun Liu, Yongquan Chen, Yalan Chen, Yuxin Lin, Yan Sun, Bairong Shen:
CHDGKB: a knowledgebase for systematic understanding of genetic variations associated with non-syndromic congenital heart disease. Database J. Biol. Databases Curation 2020 (2020) - [j28]Chunjiang Yu, Xin Qi, Yuxin Lin, Yin Li, Bairong Shen:
iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J. Biomed. Informatics 112: 103605 (2020)
2010 – 2019
- 2019
- [j27]Fei Ye, Fei Zhu, Yuchen Fu, Bairong Shen:
ECG Generation With Sequence Generative Adversarial Nets Optimized by Policy Gradient. IEEE Access 7: 159369-159378 (2019) - [j26]Yuxin Lin, Fuliang Qian, Li Shen, Feifei Chen, Jiajia Chen, Bairong Shen:
Computer-aided biomarker discovery for precision medicine: data resources, models and applications. Briefings Bioinform. 20(3): 952-975 (2019) - [j25]Chaoying Zhan, Manhong Shi, Rongrong Wu, Hongxin He, Xingyun Liu, Bairong Shen:
MIRKB: a myocardial infarction risk knowledge base. Database J. Biol. Databases Curation 2019: baz125 (2019) - [j24]Bairong Shen, Yuxin Lin, Cheng Bi, Shengrong Zhou, Zhongchen Bai, Guangmin Zheng, Jing Zhou:
Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations. Genom. Proteom. Bioinform. 17(4): 415-429 (2019) - [j23]Bairong Shen, Xiaoqian Jiang, Xingming Zhao:
Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare. IEEE ACM Trans. Comput. Biol. Bioinform. 16(1): 91-92 (2019) - 2018
- [j22]Yang Yang, Chen Xu, Xingyun Liu, Chao Xu, Yuanyuan Zhang, Li Shen, Mauno Vihinen, Bairong Shen:
NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database. Database J. Biol. Databases Curation 2018: bay018 (2018) - [j21]Xueli Zhang, Xiao-Feng Sun, Yang Cao, Benchen Ye, Qiliang Peng, Xingyun Liu, Bairong Shen, Hong Zhang:
CBD: a biomarker database for colorectal cancer. Database J. Biol. Databases Curation 2018: bay046 (2018) - [j20]Wenying Yan, Guang Hu, Zhongjie Liang, Jianhong Zhou, Yang Yang, Jiajia Chen, Bairong Shen:
Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues. J. Chem. Inf. Model. 58(9): 2024-2032 (2018) - [j19]Chunjiang Yu, Wentao Wu, Jing Wang, Yuxin Lin, Yang Yang, Jiajia Chen, Fei Zhu, Bairong Shen:
NGS-FC: A Next-Generation Sequencing Data Format Converter. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1683-1691 (2018) - [c9]Jianhong Zhou, Christopher J. Oldfield, Fei Huang, Wenying Yan, Bairong Shen, A. Keith Dunker:
Identification of intrinsic disorder in complexes from Protein Data Bank. ICCABS 2018: 1 - 2016
- [j18]Yang Yang, Abhishek Niroula, Bairong Shen, Mauno Vihinen:
PON-Sol: prediction of effects of amino acid substitutions on protein solubility. Bioinform. 32(13): 2032-2034 (2016) - [j17]Feixiong Cheng, Chuang Liu, Bairong Shen, Zhongming Zhao:
Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst. Biol. 10(S-3): 65 (2016) - 2015
- [j16]Jiajia Chen, Maomin Sun, Bairong Shen:
Deciphering oncogenic drivers: from single genes to integrated pathways. Briefings Bioinform. 16(3): 413-428 (2015) - [c8]Fei Zhu, Quan Liu, Xiaofang Zhang, Bairong Shen:
Protein-Protein Interaction Network Constructing Based on Text Mining and Reinforcement Learning with Application to Prostate Cancer. TrustCom/BigDataSE/ISPA (1) 2015: 1306-1311 - 2014
- [c7]Fei Zhu, Quan Liu, Xiaofang Zhang, Bairong Shen:
Protein-protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer. BIBM 2014: 46-51 - 2013
- [j15]Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen:
Identifying novel glioma associated pathways based on systems biology level meta-analysis. BMC Syst. Biol. 7(S-2): S9 (2013) - [j14]Christian Schönbach, Bairong Shen, Tin Wee Tan, Shoba Ranganathan:
InCoB2013 introduces Systems Biology as a major conference theme. BMC Syst. Biol. 7(S-3): S1 (2013) - [j13]Yifei Tang, Wenying Yan, Jiajia Chen, Cheng Luo, Antti Kaipia, Bairong Shen:
Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer. BMC Syst. Biol. 7(S-3): S6 (2013) - [j12]Bairong Shen, Hong-Bin Shen, Tianhai Tian, Qiang Lü, Guang Hu:
Translational Bioinformatics and Computational Systems Medicine. Comput. Math. Methods Medicine 2013: 375641:1-375641:2 (2013) - [j11]Jiajia Chen, Ying Wang, Bairong Shen, Daqing Zhang:
Molecular Signature of Cancer at Gene Level or Pathway Level? Case Studies of Colorectal Cancer and Prostate Cancer Microarray Data. Comput. Math. Methods Medicine 2013: 909525:1-909525:8 (2013) - [j10]Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan H. Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen:
Biomedical text mining and its applications in cancer research. J. Biomed. Informatics 46(2): 200-211 (2013) - 2012
- [j9]Chao Xu, Jiajia Chen, Bairong Shen:
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? BMC Syst. Biol. 6(S-1): S21 (2012) - [j8]Min Ding, Haiyun Wang, Jiajia Chen, Bairong Shen, Zhonghua Xu:
Identification and Functional Annotation of Genome-Wide ER-Regulated Genes in Breast Cancer Based on ChIP-Seq Data. Comput. Math. Methods Medicine 2012: 568950:1-568950:10 (2012) - [c6]Jiajia Chen, Daqing Zhang, Wenyu Zhang, Yifei Tang, Lingchuan Guo, Bairong Shen:
An integrative framework for identifying consistent microRNA expression signatures associated with clear cell renal cell carcinoma. ISB 2012: 37-42 - [c5]Yangfan Hu, Jinquan Li, Jiajia Chen, Guang Hu, Bairong Shen:
Identifying novel glioma associated pathways based on integrated 'omics' data. ISB 2012: 49-55 - [c4]Preecha Patumcharoenpol, Jonathan Hoyin Chan, Asawin Meechai, Bairong Shen, Wanwipa Vongsangnak:
Bibliome Mining Platform and Application for Building Metabolic Interaction Network. CSBio 2012: 55-62 - 2011
- [j7]Bingchuan Liu, Jiajia Chen, Bairong Shen:
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC Syst. Biol. 5(S-1): S2 (2011) - [j6]Ying Wang, Jiajia Chen, Qinghui Li, Haiyun Wang, Ganqiang Liu, Qing Jing, Bairong Shen:
Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Comput. Biol. Chem. 35(3): 151-158 (2011) - 2010
- [j5]Binhua Tang, Xuechen Wu, Ge Tan, Su-Shing Chen, Qing Jing, Bairong Shen:
Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. BMC Syst. Biol. 4(S-2): S3 (2010) - [j4]Ganqiang Liu, Min Ding, Haiyun Wang, Jinyan Huang, Qing Jing, Bairong Shen:
Pathway analysis of microRNAs in mouse heart development. Int. J. Bioinform. Res. Appl. 6(1): 12-20 (2010) - [c3]Sushing Chen, Bairong Shen, Jiajia Chen, Yang Yang, Yuan Li:
Traditional Chinese Medicine data mining: Associating clinical cancer case studies with Traditional Chinese Medicine therapies. BIBM Workshops 2010: 648-650
2000 – 2009
- 2009
- [j3]Binhua Tang, Li He, Qing Jing, Bairong Shen:
Model-Based Identification and Adaptive Control of the Core Module in a Typical Cell Cycle Pathway via Network and System Control Theories. Adv. Complex Syst. 12(1): 21-43 (2009) - [c2]Haiyun Wang, Min Ding, Xia Li, Bairong Shen:
Clinical Information Driven Ensemble Clustering for Inferring Robust Tumor Subtypes. BMEI 2009: 1-4 - 2008
- [j2]Haiyun Wang, Qi Wang, Xia Li, Bairong Shen, Min Ding, Ziyin Shen:
Towards patterns tree of gene coexpression in eukaryotic species. Bioinform. 24(11): 1367-1373 (2008) - 2007
- [c1]Binhua Tang, Li He, Sushing Chen, Bairong Shen:
System Stability Via Stepping Optimal Control: Theory and Applications. EPIA Workshops 2007: 463-472 - 2003
- [j1]Bairong Shen, Mauno Vihinen:
RankViaContact: ranking and visualization of amino acid contacts. Bioinform. 19(16): 2161-2162 (2003)
Coauthor Index
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